user can setup seed in bass file now, if he does not specify any value for seed, oopse will take the value of seconds of system time as seed
updated the Changelog. added some bug fixes for setting the random number generator seed value. fixed a bug where ghostbend atom b was not being set. ( recent bug from SimState conversion)
reformmating ZConstraint and fixe bug of error msg printing
Tested MPI version of Z-Constraint Method
harmonic potential & z-contraint method
fixed a really annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location.
debugging globals
added harmonical potential to z-constraint method
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switched SimInfo to use a system configuration from SimState rather than arrays from Atom
stable version of Z-Constraint
add index range checking into ZConstraint
Added Z constraint.
working on the props code
Added eam to simSetup and added changecutoffeam.
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Fixed a current time initialization bug in InitFromFile.
Changed how cutoffs were handled from C. Now notifyCutoffs in Fortran notifies those who need the information of any changes to cutoffs.
more fixes for box changes
cleaned up simSetup
fixed some bugs, Changed entry_plug to info where appropriate
Bugfix in NPTim, fixes for NPTfm
Checking in changes for NPTim
Bug fixing NPTi and NPTf. there is some error in the caclulation of HmatInverse.
adding in dan's NPT stuff
Fixes and merging NPTf
fixed the bugs introduced by switching the periodic box to a matrix
Changed over the bonds to Harmonic bonds in the DUFF frc file fixed constraints.
Most of the integrator and NVT seem to be working now.
finished the basics of the integrator and SimSetup.cpp
doing some work on SimSetup to clean it up / get it to work with the new Integrator.
Added Teng's parmeters fro the ghost Bend in TraPPE_Ex some work on the integrator. ( incomplete)
fixed up sysBuild to where it should now build our systems
fixed a memory bug in Fortran, where molMembershipArray was declared nLocal instead of nGlobal.
Bug fix in progress for NPT
added a globalIndex counter to Molecule
fixed a n mpi init bug in SimSetup. caused a miscalculation of nLocal.
fixes for NPT and NVT
Fixes for NPT / NVT
Fixes for NPT and NVT
bug fixes
Added ExtendedSystem infrastructure for NPT and NVT calculations
dipoles mostly work, but there is a memory leak somewhere.
Fixes in MPI force calc and in Trappe_Ex parsing.
fixed a bug where the Excludes were not being created properly
mpi fixes and debugging mpi read write from file.
MPI buggy, fixed mpiRefresh issue.
fixed a bug where excludes were not being initialized
Fixed a single processor segfault bug.
fixed a few more bugs.
fixing some compile time bugs
finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class
LJ_FF has been converted to the new Molecule model. TraPPE_Ex is currently being updated. SimSetups routines are writtten, but not yet called.
the skeleton for making the molecules is in place. ForceField needs to be updated next.
still working on the SimSetup routine. also fixed some things in Exclude.hpp
I'm overhauling the molecule class to contain it's own bonds, bends, and torsions. may god have mercy on my soul.
electrostatic changes for dipole / RF separation
This commit was generated by cvs2svn to compensate for changes in r377, which included commits to RCS files with non-trunk default branches.
New OOPSE Tree
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